Alignments for a candidate for mmsB in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Herbaspirillum seropedicae SmR1

Align 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (characterized)
to candidate HSERO_RS15390 HSERO_RS15390 3-hydroxyisobutyrate dehydrogenase

Query= SwissProt::P28811
         (298 letters)



>FitnessBrowser__HerbieS:HSERO_RS15390
          Length = 297

 Score =  328 bits (840), Expect = 1e-94
 Identities = 172/288 (59%), Positives = 208/288 (72%), Gaps = 2/288 (0%)

Query: 3   DIAFLGLGNMGGPMAANLLKAGHRVNVFDLQPKAVLGLVEQGAQGADSALQCCEGAEVVI 62
           +I F+GLGNMG PMA NL+KAG  V+  DL   +V  LVE G +    ++     A+VVI
Sbjct: 4   NIVFIGLGNMGLPMAQNLVKAGFSVSGHDLVKASVDKLVEVGGKTEADSMAAVAKADVVI 63

Query: 63  SMLPAGQHVESLYLGDDGLLARVAGKPLLIDCSTIAPETARKVAEAAAAKGLTLLDAPVS 122
           +MLPA +HVESLYLG+ G+LA      LLIDCSTIAPE ARKVA AA A+G  +LDAPVS
Sbjct: 64  TMLPASRHVESLYLGEAGVLASAKPGTLLIDCSTIAPEAARKVAAAAKARGFEMLDAPVS 123

Query: 123 GGVGGARAGTLSFIVGGPAEGFARARPVLENMGRNIFHAGDHGAGQVAKICNNMLLGILM 182
           GG  GA AGTL+F+VGG  E F  A+P L+ MG+ I+HAG+ G+GQ  K+CNNMLLGILM
Sbjct: 124 GGTNGATAGTLTFMVGGSKEAFEAAQPYLQKMGKAIYHAGESGSGQTVKVCNNMLLGILM 183

Query: 183 AGTAEALALGVKNGLDPAVLSEVMKQSSGGNWALNLYNPWPGVMPQAPASNGYAGGFQVR 242
            GT+EA+ LG+ NG+DP VLSE+M +SSG NW L +YNP PGVM  APAS GYAGGF V 
Sbjct: 184 IGTSEAIRLGMANGMDPKVLSEIMSKSSGRNWTLEVYNPCPGVMETAPASKGYAGGFGVD 243

Query: 243 LMNKDLGLALANAQAVQASTPLGALARNLFSLHAQADAEHEGLDFSSI 290
           LM KDLGLA+ NA A   + PLGA ARNL+ +H+   A    LDFSSI
Sbjct: 244 LMLKDLGLAVENALATNCAIPLGATARNLYDIHSMNGAGK--LDFSSI 289


Lambda     K      H
   0.317    0.135    0.395 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 313
Number of extensions: 15
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 298
Length of database: 297
Length adjustment: 26
Effective length of query: 272
Effective length of database: 271
Effective search space:    73712
Effective search space used:    73712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate HSERO_RS15390 HSERO_RS15390 (3-hydroxyisobutyrate dehydrogenase)
to HMM TIGR01692 (mmsB: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01692.hmm
# target sequence database:        /tmp/gapView.4332.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01692  [M=288]
Accession:   TIGR01692
Description: HIBADH: 3-hydroxyisobutyrate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                  Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
     3e-127  409.9  10.1   3.4e-127  409.7  10.1    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS15390  HSERO_RS15390 3-hydroxyisobutyra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS15390  HSERO_RS15390 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.7  10.1  3.4e-127  3.4e-127       1     287 [.       7     293 ..       7     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 409.7 bits;  conditional E-value: 3.4e-127
                                  TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhves 68 
                                                fiGlGnmG pma+nl+kag++v+ +dl  + v++lve G ++ a +++av++advvitmlPa++hves
  lcl|FitnessBrowser__HerbieS:HSERO_RS15390   7 FIGLGNMGLPMAQNLVKAGFSVSGHDLVKASVDKLVEVGGKTEADSMAAVAKADVVITMLPASRHVES 74 
                                                9*************************************99999999999******************* PP

                                  TIGR01692  69 vyagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgea 136
                                                +y+g+ g+la +k ++llid+sti++++arkva++a+a+G+ +ldaPvsGG+ ga aGtltfmvGg++
  lcl|FitnessBrowser__HerbieS:HSERO_RS15390  75 LYLGEAGVLASAKPGTLLIDCSTIAPEAARKVAAAAKARGFEMLDAPVSGGTNGATAGTLTFMVGGSK 142
                                                ******************************************************************** PP

                                  TIGR01692 137 eefaraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilsks 204
                                                e+f++a+p l+ mgk i haG++G+Gq+ k+Cnn+llgi miG++ea+ lg+++G+dpkvl+ei+sks
  lcl|FitnessBrowser__HerbieS:HSERO_RS15390 143 EAFEAAQPYLQKMGKAIYHAGESGSGQTVKVCNNMLLGILMIGTSEAIRLGMANGMDPKVLSEIMSKS 210
                                                ******************************************************************** PP

                                  TIGR01692 205 sGrcWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfas 272
                                                sGr+W+l+ ynP PGv+e+aPas+gy+gGf+++lmlkdlgla e+a +++  ++lGa+ar+ly +++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS15390 211 SGRNWTLEVYNPCPGVMETAPASKGYAGGFGVDLMLKDLGLAVENALATNCAIPLGATARNLYDIHSM 278
                                                ******************************************************************** PP

                                  TIGR01692 273 kgagkkdfsavikll 287
                                                +gagk+dfs+++++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS15390 279 NGAGKLDFSSIFNML 293
                                                ************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (297 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.54
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources